Paired Multiome samples

[icenzano]

Hello everyone! I am starting with multi-omics analysis and I need to analyze our three 10x multi-omics datasets with ArchR. However, I am not sure about the correct order to follow. If I have multiple samples, which is the correct approach?

1. Should I integrate RNA samples and ATAC samples separately using Harmony (or any other batch correction method) and then combine/integrate both omics layers using the batch corrected dimension coming from each omic?
2. Or, should I integrate both omics layers first and then correct the batch effect coming from having three samples using Harmony (or any other batch correction method) within the combined dimension?
   Thank you.